Creating Awesome Plots with ggplot2

A ggplot needs 3 parts:

1. data
2. aesthetics which connect or map the data to the geom
3. a type of plot, or geom, to implement

Note:

• ggplot2 uses the + notation in their plots (see below). I think there is some regret over this style decision, but it is now an accepted convention!
  
• ggplot2 also uses non-standard evaluation, so, often column names do not need to be quoted
  
• common mapping aesthetics:
  • x (the x variable)
    
  • y (the y variable)
    
  • col (color for lines, points, outlines)
    
  • fill (color when something has a fill color such as a boxplot)
    
  • group (when a plotted option should be grouped, then plotted)

Step 1: Add the data

ggplot(hay_idaho)

(not much to see here - we have not specified the aesthetics or the geom)

Step 2: Add aesthetics

ggplot(hay_idaho, mapping = aes(x = year, y = yield))

This step mapped “year” and “yield” from the hay_idaho data set to the x and y axes, respectively. Nothing is plotted because we have not specified what type of plot geom we want.

Step 3: Add a geom

(explicit mapping command dropped - use a positional argument instead)

ggplot(hay_idaho, aes(x = year, y = yield)) +
  geom_line()

Question: What happens if we use %>% instead of +?

plot title and axis labels

ggplot(hay_idaho, aes(x = year, y = yield)) +
  geom_line() +
  ggtitle("Total historic hay yields in Idaho") + 
  xlab("Year") +
  ylab("yield (1000s of tons)")

Change line settings

(and other geom arguments)

ggplot(hay_idaho, aes(x = year, y = yield)) +
  geom_line(color = "turquoise", size = 1.5, linetype = 1) +
  ggtitle("Total historic hay yields in Idaho") + 
  xlab("Year") +
  ylab("yield (1000's of tons)")

The default line type is “1”, which is a plain line. There are other types:

points

ggplot(hay_idaho, aes(x = year, y = yield)) +
  geom_point(shape = 2, col = "navy") +
  ggtitle("Total historic hay yields in Idaho") + 
  xlab("Year") +
  ylab("yield (1000s of tons)")

There are many options for the type of plotting character (“pch” in base R plotting and “shape” in ggplot):

The default shape is “1” (the circle). Plotting symbols 21 - 25 have outline color and fill attributes, while the other symbols only take a single color argument.

area

ggplot(hay_idaho, aes(x = year, y = yield)) +
  geom_area(fill = "orange", col = "gray20") +
  ggtitle("Total historic hay yields in Idaho") + 
  xlab("Year") +
  ylab("yield (1000s of tons)")

boxplot

ggplot(hay_pnw, aes(x = state, y = yield)) +
  geom_boxplot() +
  ggtitle("Yearly hay yields in the Pacific Northwest") + 
  xlab("State") +
  ylab("yield (1000s of tons)")

Color all boxplots the same:

ggplot(hay_pnw, aes(x = state, y = yield)) +
  geom_boxplot(fill = "yellow") +
  ggtitle("Yearly hay yields in the Pacific Northwest") + 
  xlab("State") +
  ylab("yield (1000s of tons)")

Color boxplots by state:
(This requires an aes statement.)

ggplot(hay_pnw, aes(x = state, y = yield, fill = state)) +
  geom_boxplot() +
  ggtitle("Yearly hay yields in the Pacific Northwest") + 
  xlab("State") +
  ylab("yield (1000s of tons)")

Question: What happens if we specify “color = state” instead of “fill = state”?

histograms and density plots:

ggplot(hay_idaho, aes(x = yield)) +
  geom_histogram(fill = "gray70", col = "black", bins = 20)

## Warning: Removed 1 rows containing non-finite values (stat_bin).

Unlike in base R plotting, creating a density plot and shading the are under the curve is easy.

ggplot(hay_pnw, aes(x = yield, fill = state)) +
  geom_density()

In this plot, it is hard to see what is going on since the each distribution covers up the one plotted before it (so we can’t really see Idaho, but Washington’s hay yield distribution is clear). The attribute “alpha” can be used to add a transparency to colors. The code is alpha = n where n is the proportion of the color that is shown (0 is completely transparent and 1 is no transparency).

ggplot(hay_pnw, aes(x = yield, fill = state)) +
  geom_density(alpha = 0.5)

Combining geoms

Geoms are best thought of as plotting layers. Additional geoms can be added to a single plot, adding additional layers of information. Each geom is added to the plot in the order it is specified in the ggplot statement.

Adding an overall of points over boxplots is a good way to summarise the empirical distribution of a large number of data points:

ggplot(hay_pnw, aes(x = state, y = yield, fill = state)) +
  geom_boxplot() +
  geom_point() +
  ggtitle("Yearly hay yields in the Pacific Northwest") + 
  xlab("State") +
  ylab("yield (1000s of tons)")

In this example, it is likely there is over-plotting of data since each state has 104 data point associated with it. The geom geom_jitter() can be used to jiggle overlapping points. Points can be jittered in the vertical and horizontal direction. In this case, jittering in the horizontal direction will result in no change in the interpretation since the y-axis indicates actual value associated with each point.

ggplot(hay_pnw, aes(x = state, y = yield, fill = state)) +
  geom_boxplot() +
  geom_jitter(width = 0.3, height = 0) +
  ggtitle("Yearly hay yields in the Pacific Northwest") + 
  xlab("State") +
  ylab("yield (1000s of tons)")

Faceting

Sometimes, it is useful to create a set of similar plots with the same scaling. Facets are useful for this purpose.

For an example, below is a plot of the distributions from above using facet_grid().

ggplot(hay_pnw, aes(x = yield)) +
  geom_density(col = "blue", fill = "dodgerblue", alpha = 0.6) +
  facet_grid(. ~ state) # for a horizontal facet

ggplot(hay_pnw, aes(x = yield)) +
  geom_density(col = "darkgreen", fill = "springgreen3", alpha = 0.6) +
  facet_grid(state ~ .) # for a vertical facet

Faceting can also be done be used to create a grid of plots with facet_wrap():

ggplot(hay_pnw) +
  geom_line(aes(x = year, y = yield), col = "darkcyan") +
  facet_wrap(. ~ state, nrow = 2, ncol = 2)

Representing error information

Example: create a band indicates the minimum and maximum range of values

hay_yearly <- nass.hay %>% group_by(year) %>% 
  summarise(Yield = mean(yield), yield_min = min(yield), yield_max = max(yield))

ggplot(hay_yearly, aes(x = year)) + 
  geom_ribbon(aes(ymin = yield_min, ymax = yield_max), fill = "gray70") +
  geom_line(aes(y = Yield), size = 0.8)

Example: add error bars

Two other plot adjustments included: * indicate the range of numbers that the y-axis should span * flip the x and y axes

hay_pnw_summary <- hay_pnw %>% group_by(state) %>% 
  summarise(Yield = mean(yield, na.rm = T), yield_sd = sd(yield, na.rm = T))

ggplot(hay_pnw_summary, aes(x = state)) + 
  geom_errorbar(aes(ymin = Yield - yield_sd, ymax = Yield + yield_sd), width = 0.2) +
  geom_point(aes(y = Yield), shape = 18, size = 5, col = "blue") +
  ylim(c(0, 3.7)) +
  coord_flip()

Add regression lines to a plot

P <- ggplot(hay_idaho, aes(x = acres, y = yield)) +
  geom_point(shape = 16, alpha = 0.6, size = 2.5)
P  # Plots can be assigned to an object and then later added to

P +
  geom_smooth(method = "lm") +
  geom_smooth(method = "loess", col = "yellowgreen")

Implementing a ggplot theme

facet.plot <- ggplot(hay_pnw) +
  geom_line(aes(x = year, y = yield), col = "darkcyan") +
  facet_wrap(. ~ state, nrow = 2, ncol = 2)

facet.plot + theme_minimal() 

This is not exactly what I want. Larger labels on everything would be helpful, as well as an outline around each plot. And while we are at it, labeling the x-axis for each decade rather than every 25 years would be easier to interpret.

Adjusting text size

facet.plot + 
  theme_minimal() +   # this must be added to plot before manual theme adjustments 
  theme(
   axis.title = element_text(size = 14),
   axis.text = element_text(size = 13)
 )

Adjusting the axis and gridlines

facet.plot + 
  scale_x_continuous(breaks = c(seq(1910, 2015, by = 10)))  +
  theme_minimal() + 
   theme(
     axis.title = element_text(size = 14),
     axis.text = element_text(size = 13)
   ) 

It looks like the years are spaced too close together and there are too many grid lines. This can all be fixed.

facet.plot + 
  scale_x_continuous(breaks = c(seq(1910, 2015, by = 10)))  +
  theme_minimal() + # this must be added to plot before manual theme adjustments 
   theme(
     axis.title = element_text(size = 14),  # adsjut title of the axes
     axis.text = element_text(size = 13),  # adjust axes tick labels
     axis.text.x = element_text(angle = 45, hjust = 1), # adjust individual axis tick labels 
     panel.grid.minor = element_blank(),  # remove minor grid lines (the major grid lines were retained)
     panel.border = element_rect(colour = "black", fill = "transparent"), # create a border around each panel
     strip.text = element_text(size = 15) # adjust panel labels (e.g. "Idaho")
   ) 

Adjusting the legend

ggplot(hay_pnw) +
  geom_line(aes(x = year, y = yield, col = state)) +
  scale_x_continuous(breaks = c(seq(1910, 2015, by = 10)))  +
  theme_bw() 

This looks okay, but it could be better. There is room to put the legend inside the plot and the text should probably be larger. Also, the legend title is not really needed.

ggplot(hay_pnw) +
  geom_line(aes(x = year, y = yield, col = state)) +
  scale_x_continuous(breaks = c(seq(1910, 2015, by = 10)))  +
  theme_bw() +
  theme(
    legend.position = c(0.15, 0.8), # give exact coordinates (ranging from 0 to 1)
    legend.background = element_rect(colour = "black"),
    legend.text = element_text(size = 12),
    legend.title = element_blank()
  )

The legend can also be moved to locations outside the main plotting area with arguments such as legend.position = "top", legend.position = "left" and so on.

Summary

There are many options for adjusting text. You you will inevitable need to consult help files at some point.

How to save plots

• The function ggsave() is the recommended approach.
• By default, it will save the the last plot created.

ggplot(hay_pnw) +
  geom_line(aes(x = year, y = yield), col = "violetred") +
  facet_wrap(. ~ state, nrow = 2, ncol = 2)

ggsave("PNW_hay_production.png", dpi = 400)

## Saving 7 x 5 in image

• other acceptable formats:
  • .jpeg
  • .tiff
  • .bmp
  • .svg
  • .wmf (on windows machines)
  • .pdf
  • .eps
  • .ps
  • .tex
  • .pd
• can specify the size of the saved plot (in centimeters, millimeters or inches) and the resolution in DPI (dots per square inch)

Other great geoms

ggridge

# break hay data into decennial increments (roughly)
nass.hay$decade <- cut(nass.hay$year, breaks = c(1900, 1920, 1930, 1940, 1950, 1960, 1970, 1980, 1990, 2000, 2020), labels = c("pre-1920", "1920s", "1930s", "1940s", "1950s", "1960s", "1970s", "1980s", "1990s", "2000s"))

library(ggridges); library(viridis)

## 
## Attaching package: 'ggridges'

## The following object is masked from 'package:ggplot2':
## 
##     scale_discrete_manual

## Loading required package: viridisLite

ggplot(nass.hay, aes(x = yield, y = reorder(decade, desc(decade)), fill = ..x..)) +
  geom_density_ridges_gradient(rel_min_height = 0.001) +
  scale_fill_viridis(direction = -1) + 
  ylab("") # suppress the y-axis label

## Picking joint bandwidth of 0.129

plotly

library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

pl <- ggplot(nass.hay, aes(x = acres, y = yield, color = year)) +
  geom_point() +
  geom_point(aes(text = state)) + 
  #, shape = 21, col = "gray30", alpha = 0.6) +
  #scale_fill_manual(values = alpha(rainbow(nlevels(nass.hay$state)), 0.5))
  scale_color_gradientn(colors = alpha(rainbow(20), 0.5))

ggplotly(pl)

To save an interactive plot, use htmlwidgets::saveWidget().

gganimate

Plot from “Learn gganimate”.